Correction: Halun et al. Investigation of Ring and Star Polymers in Confined Geometries: Theory and Simulations. Entropy 2021, 23, 242.

The authors wish to make the following correction to this paper [...].

Investigation of Ring and Star Polymers in Confined Geometries: Theory and Simulations.

The calculations of the dimensionless layer monomer density profiles for a dilute solution of phantom ideal ring polymer chains and star polymers with f=4 arms in a Θ-solvent confined in a slit geometry of two parallel walls with repulsive surfaces and for the mixed case of one repulsive and the other inert surface were performed. Furthermore, taking into account the Derjaguin approximation, the dimensionless layer monomer density profiles for phantom ideal ring polymer chains and star polymers immersed in a solution of big colloidal particles with different adsorbing or repelling properties with respect to polymers were calculated. The density-force relation for the above-mentioned cases was analyzed, and the universal amplitude ratio B was obtained. Taking into account the small sphere expansion allowed obtaining the monomer density profiles for a dilute solution of phantom ideal ring polymers immersed in a solution of small spherical particles, or nano-particles of finite size, which are much smaller than the polymer size and the other characteristic mesoscopic length of the system. We performed molecular dynamics simulations of a dilute solution of linear, ring, and star-shaped polymers with N=300, 300 (360), and 1201 (4 × 300 + 1-star polymer with four arms) beads accordingly. The obtained analytical and numerical results for phantom ring and star polymers are compared with the results for linear polymer chains in confined geometries.

Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs.

We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat. The key enhancements over Ensembl funcgen include the following: (i) a user can add private data, analyze them alongside the public data and manage access rights; (ii) inside the database, we provide efficient procedures for computing intersections between regulatory features and for mapping them to the genes. To Ensembl funcgen-derived data, which include data from ENCODE, we add information on conserved non-coding (putative regulatory) sequences, and on genome-wide occurrence of transcription factor binding site motifs from the current versions of two major motif libraries, namely, Jaspar and Transfac. The intersections and mapping to the genes are pre-computed for the public data, and the result of any procedure run on the data added by the users is stored back into the database, thus incrementally increasing the body of pre-computed data. As the Ensembl funcgen schema for the rat is currently not populated, our database is the first database of regulatory features for this frequently used laboratory animal. The database is accessible without registration using the mysql client: mysql -h database.nencki-genomics.org -u public. Registration is required only to add or access private data. A WSDL webservice provides access to the database from any SOAP client, including the Taverna Workbench with a graphical user interface.